To successfully insert a microprobe into the brain, it must be stiff enough to tolerate the penetration force. In contrast, due to the brain micromotion during the use of the microprobe (operation), the mechanical mismatch between the stiff microprobe and soft surrounding neural tissue leads to tissue damage and, ultimately, the failure of the microprobe. In this study, an innovative design is proposed to create a binary stiffness compliant neural microprobe. The microprobe and surrounding neural tissue are simulated to calculate the microprobe’s equivalent elastic moduli and critical buckling force. Moreover, the induced strain on the tissue by the brain longitudinal and lateral micromotions is investigated based on the finite element method. To evaluate the microprobe’s efficiency compared to existing ones, the simulation is replicated for a cylindrical microprobe with the same diameter and length, fabricated from polyimide and coated with a neuro-integrative material. Based on the obtained results, the proposed microprobe’s elastic modulus drops from ≈ 4.2 GPa during insertion to ≈ 40 kPa during operation, depending on the force/motion applied. The corresponding critical buckling force is ≈ 267 mN. The maximum strain on the tissue around the proposed microprobe is ≈ 13% and ≈ 69% less than that of the polyimide microprobe, completely bonded to the surrounding tissue, during the brain longitudinal and lateral motions, respectively. The microprobe is fabricated based on two-photon polymerisation technology, characterised, and inserted into a lamb brain to confirm the feasibility of the proposed design. The proposed microprobe’s stiffness changes independently of its material and the surrounding environment’s characteristics.